Biology subjects

Paetzold, C.

Publications and source records attributed to Paetzold, C..

4 recordsLinked to original sources

bioRxiv2023

Efficient hybrid strategies for assembling the plastome, mitochondriome, and large nuclear genome of diploid Ranunculus cassubicifolius (Ranunculaceae)

Currently, it is still a challenge - in terms of laboratory effort and cost, as well as assembly quality - to unravel the sequence of large and complex genomes from non-model plants. This often hampers the study of evolutionarily intricate species groups. The species-rich genus Ranunculus (Ranunculaceae) is an angiosperm model system for the study of polyploidy, apomixis, reticulate evolution, and biogeography. However, neither mitochondrial, nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) or PacBio/HiFi long-read, and hybrid-read assembly strategies. We used the diploid progenitor species R. cassubicifolius (R. auricomus complex), and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome, we favored a PacBio-based assembly three-times polished with filtered reads and subsequently scaffolded into 8 pseudochromosomes by chromatin conformation data (Hi-C) as the representative sequence. We obtained a haploid genome sequence with 2.69 Gbp, 94.5% complete BUSCO embryophyta_odb10 genes found, and 31,322 annotated genes. The genomic information presented here will improve phylogenomic analyses in this species complex, and will enable advanced functional, evolutionary, and biogeographic analyses for the genus and beyond Ranunculaceae in the future. Significance StatementThe genus Ranunculus is a model system in flowering plants for polyploidy, apomixis, evolution, and biogeography research. We present the first nuclear and mitochondrial genome sequence, and the plastid evolution of Ranunculaceae. Using Illumina, ONT, and PacBio data, we developed an efficient assembly strategy that can be applied to other non-model plants. Results presented here are useful for improving population genomic and phylogenomic analyses, and enable better functional analyses at species, genus and family level.

genomics↗

bioRxiv2021

Unraveling phylogenetic relationships, reticulate evolution, and genome composition of polyploid plant complexes by RAD-Seq and Hyb-Seq

Complex genome evolution of young polyploid complexes is poorly understood. Besides challenges caused by hybridization, polyploidization, and incomplete lineage sorting, bioinformatic analyses are often exacerbated by missing information on progenitors, ploidy, and reproduction modes. By using a comprehensive, self-developed bioinformatic pipeline integrating phylogenetic, structure, network, and SNP-origin analyses, we for the first time unraveled polyploid phylogenetic relationships and genome evolution within the large Eurasian Ranunculus auricomus species complex comprising more than 840 taxa. Our results rely on 97,312 genomic RAD-Seq loci, target enrichment of 576 nuclear genes (48 phased), and 71 plastid regions (Hyb-Seq; OMICS-data) derived from the 75 most widespread polyploid apomictic taxa and four di- and one tetraploid potential sexual progenitor species. Phylogenetic tree and structure analyses consistently showed 3-5 supported polyploid groups, each containing sexual progenitor species. In total, analyses revealed four diploid sexual progenitors and a one unknown, probably extinct progenitor, contributing to the genome composition of R. auricomus polyploids. Phylogenetic network, structure, and SNP-origin analyses based on RAD-Seq loci and phased nuclear genes completed by plastid data demonstrated predominantly allopolyploid origins, each involving 2-3 different diploid sexual subgenomes. Allotetraploid genomes were characterized by subgenome dominance and large proportions of interspecific, non-hybrid SNPs, indicating an enormous degree of post-origin evolution (i.e., Mendelian segregation of the diploid hybrid generations, back-crossings, and gene flow due to facultative sexuality of apomicts), but only low proportions of lineage-specific SNPs. The R. auricomus model system is the first large European polyploid species complex studied with reduced representation OMICS data. Our bioinformatic pipeline underlines the importance of combining different approaches and datasets to successfully unveil how reticulate evolution and post-origin processes shape the diversity of polyploid plant complexes.

evolutionary biology↗

bioRxiv2021

Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events

Background and aimsZanthoxylum L. is the only pantropical genus within Rutaceae, with a few species native to temperate eastern Asia and North America. Efforts using Sanger sequencing failed to resolve the backbone phylogeny of Zanthoxylum. In this study, we employed target enrichment high-throughput sequencing to improve resolution. Gene trees were examined for concordance and sectional classifications of Zanthoxylum were evaluated. Off-target reads were investigated to identify putative single-copy markers for bait refinement, and low-copy markers for evidence of putative hybridization events. MethodsWe developed a custom bait set for target enrichment of 745 exons in Zanthoxylum and applied it to 45 Zanthoxylum species and one Tetradium species as the outgroup. Illumina reads were processed via the HybPhyloMaker pipeline. Phylogenetic inferences were conducted using coalescent and concatenated methods. Concordance was assessed using quartet sampling. Off-target reads were assembled and putative single- and low-copy genes were extracted. Additional phylogenetic analyses were performed based on these alignments. Key resultsFour major clades are supported within Zanthoxylum: the African clade, the Z. asiaticum clade, the Asian-Pacific-Australian clade, and the American-eastern Asian clade. While overall support has improved, regions of conflict are similar to those previously observed. Gene tree discordances indicate a hybridization event in the ancestor of the Hawaiian lineage, and incomplete lineage sorting for the American backbone. Off-target putative single-copy genes largely confirm on-target results, and putative low-copy genes provide additional evidence for hybridization in the Hawaiian lineage. Only two of the five sections of Zanthoxylum are resolved as monophyletic. ConclusionTarget enrichment is suitable to assess phylogenetic relationships in Zanthoxylum. Our phylogenetic analyses reveal that current sectional classifications need revision. Quartet tree concordance indicates several instances of reticulate evolution. Off-target reads are proven useful to identify additional phylogenetically informative regions for bait refinement or gene tree based approaches.

evolutionary biology↗

bioRxiv2020

Phylogenomics unravels speciation patterns in temperate-montane plant species: a case study on the recently radiating Ranunculus auricomus species complex

The time frame and geographical patterns of diversification processes in European temperate-montane herbs are still not well understood. We used the sexual species of the Ranunculus auricomus complex as a model system to understand how vicariance vs. dispersal processes in the context of Pleistocene climatic fluctuations have triggered speciation in temperate-montane plant species. We employed Target Enrichment sequence data from about 600 nuclear genes and coalescent-based species tree inference methods to resolve phylogenetic relationships among the sexual taxa of the complex. We estimated absolute divergence times and, using ancestral range reconstruction, we tested if speciation was rather enhanced by vicariance or dispersal processes. Phylogenetic relationships among taxa were fully resolved. Incongruence among species trees mainly concerned the intraspecific relationships in R. notabilis s.l., R. cassubicifolius s.l., and the position of the tetraploid R. marsicus. Speciation events took place in a very short time at the end of the Mid-Pleistocene Transition (830-580 ka). A second wave of intraspecific geographical differentiation within and around the European mountain systems happened between 200-100 ka. Ancestral range reconstruction supports the existence of a widespread European ancestor of the R. auricomus complex. Vicariance processes have triggered allopatric speciation in temperate-montane plant species during the climatic deterioration occurred in the last phase of the Mid-Pleistocene Transition. Vegetation restructuring from forest into tundra could have confined these forest species into isolated glacial refugia. During subsequent warming periods, range expansions of these locally distributed species could have been hampered by congeneric competitors in the same habitat.

evolutionary biology↗